Gnumap

Gnumap maps next-generation sequencing reads using probabilistic algorithms to quantitatively assign reads to repetitive genomic regions and to improve alignments of lower quality Solexa/Illumina reads.

Key Features:

• Probabilistic quantitative mapping: Employs a probabilistic algorithm to assign reads to repetitive genomic regions quantitatively.
• Probabilistic Needleman-Wunsch: Uses an adaptation of the Needleman-Wunsch algorithm in a probabilistic framework to improve alignment of lower quality reads.
• Solexa/Illumina file support: Processes _prb.txt and _int.txt files produced by the Solexa/Illumina sequencing pipeline.
• Improved mapping accuracy: Increases reliability and comprehensiveness of sequence data analysis by better handling repeats and low-quality reads.

Scientific Applications:

• Repeat-region read assignment: Enables quantitative assignment of reads within repetitive genomic regions for genomic analyses.
• Alignment of low-quality Solexa/Illumina reads: Enhances alignment of lower quality reads to increase usable data from next-generation sequencing experiments.
• Precise genomic analysis: Supports studies that require accurate read placement and comprehensive mapping in NGS datasets.

Methodology:

Applies a probabilistic mapping algorithm for quantitative assignment to repeats and a probabilistic adaptation of the Needleman-Wunsch algorithm that operates on _prb.txt and _int.txt files from the Solexa/Illumina pipeline.